Yes. libglade files and gtkbuilder files are two seperate animals (although they are similar, and have the same purpose).

Yes intltool-extract version 0.41.1 seems to extract gtkbuilder file strings if you give it the --type=gettext/glade option. (it seems to automatically distinguish between libglade files and gtkbuilder files)

Since I am not a GNOME developer, the situation is not clear to
me, and I need a bit of your help in order to understand what
needs to be done:
- Can you point me to some example .gtkbuilder files
(preferrably in some released tarballs or under version
control of some project)?
- Can you point me to the specification of .gtkbuilder files
(how they are meant to be structured, or the schema if it's
an XML file format).
- I see that there is a tool "gtk-builder-convert" whose job
is to convert glade files to .gtkbuilder files. So presumably
the two file types are not the same?
- Is there support for .gtkbuilder files in some intltool
revision?

Guessing the file type with libmagic is something that is too
unreliable. Let's leave this idea aside.